Background Although the risk factors associated with young people entering and becoming entrenched in street life have been thoroughly investigated, peer-reviewed evidence is scarce to nonexistent for rigorous interventions targeting social integration outcomes for young people who have experienced homelessness. From the limited research that has been done, emerging evidence signals that, although structural supports such as subsidized housing and social service providers are important, these resources alone are insufficient to help young people integrate into the mainstream society. Objective The overarching aim of this study is to assess whether and how rent subsidies and mentorship influence social integration outcomes for formerly homeless young people living in market rent housing in 3 Canadian cities. The primary outcome measures for this study are community integration (psychological and physical) and self-esteem at 18 months. Secondary outcomes include social connectedness, hope, and academic and vocational participation at 18 months. Exploratory outcomes include income, perceived housing quality, engulfment, psychiatric symptoms, and participant perspectives of intervention barriers and facilitators. Methods This is a convergent mixed methods, open-label, 2-arm parallel randomized controlled trial (RCT) with 1:1 allocation embedded within a community-based participatory action research (CBPAR) framework. The intervention will provide 24 young people (aged 16-26 years), who have transitioned out of homelessness and into market rent housing within the past year, with rent subsidies for 24 months. Half of the young people will also be randomly assigned an adult mentor who has been recruited and screened by 1 of our 3 community partners. Data collection will occur every 6 months, and participants will be followed for 30 months. Results Ethical approval for this study has been obtained from the Providence, St Joseph’s, and St Michael’s Healthcare Research Ethics Board (number 18-251). Enrollment took place from April 2019 to September 2019. Preliminary analysis of the baseline quantitative and qualitative data is underway. Conclusions This pilot RCT will be the first to test the impact of economic and social support on meaningful social integration for formerly homeless young people living in market rent housing. We believe that the mixed methods design will illuminate important contextual factors that must be considered if the intervention is to be scaled up and replicated elsewhere. Importantly, the CBPAR framework will incorporate the perspectives of the community, including formerly homeless young people, who are in the best position to determine what might work best in the context of their lives. Trial Registration Clinicaltrials.gov NCT03779204; https://clinicaltrials.gov/ct2/show/NCT03779204. International Registered Report Identifier (IRRID) DERR1-10.2196/15557